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Table 1 PAX3-FOXO1 target genes in ARMS

From: Alveolar rhabdomyosarcoma – The molecular drivers of PAX3/7-FOXO1-induced tumorigenesis

Gene

Description

Regulation

References

PF target

ABAT

4-Aminobutyrate aminotransferase;

Up

[7274]

Yes

ACTC

Actin, alpha, cardiac muscle 1

Up

[5, 75]

Yes

ADAM10

A disintegrin and metalloproteinase domain 10

Up

[73][72]

Yes

ADRA2A

Alpha-2 adrenergic receptor subtype C10

Up

[72, 74, 76]

Yes

ADRA2C

Alpha-2 adrenergic receptor subtype C4

Up

[22, 74, 76]

Yes

ALK

ALK tyrosine kinase receptor, anaplastic lymphoma kinase Ki-1

Up

[22, 72, 74, 76, 77]

Yes

ANK2

Ankyrin 2

Up

[73, 74, 76]

Yes

ASS

Argininosuccinate synthase

Up

[73, 74, 78]

?

ASTN2

Astrotactin 2

Up

[72, 76]

Yes

BIN1

Bridging integrator 1

Down

[72, 79]

Yes

BMP5

Bone morphogenic protein 5

Up

[7274, 76]

Yes

C10ORF6

Family with sequence similarity 178, member A

Up

[75, 76]

Yes

CCND1

Cyclin D1

Down

[75][79]

?

CD9

CD9 molecule/Tetraspanin-29

Up

[73, 76]

Yes

CDH3

Cadherin 3, type 1, P-cadherin (placental)

Up

[72, 76, 80]

Yes

CHD7

Chromodomain helicase DNA-binding protein 7

Up

[76, 81]

Yes

CKM

Creatine kinase M chain, muscle

Up

[5, 79]

Yes

CNR1

Cannabinoid receptor 1

Up

[22, 72, 74, 8284]

Yes

COL18A1

Collagen type 18 α 1

Up

[73, 74]

?

CXCR4

C-X-C chemokine receptor type 4

Up

[75, 76, 8587]

Yes

CXCR7

C-X-C chemokine receptor type 7

Down

[76, 87]

Yes

DCX

Neuronal migration protein doublecortin

Up

[73, 74, 81]

?

DES

Desmin

Down

[72, 79]

Yes

DKFZP762M127

Unknown

Up

[73, 74, 81]

Yes

DUSP4

Dual specificity phosphatase 4

Down

[73, 81]

?

DZIP3

DAZ interacting protein 3, zinc finger

Up

[72, 74, 81]

Yes

ELA1

Elastase-1

Up

[22, 72, 74]

Yes

ENC1

Ectodermal-neural cortex 1 (with BTB-like domain)

Up

[75, 76]

Yes

ENO3

Enolase 3 (beta, muscle)

Up

[74, 79]

?

EPHA4

Ephrin type-A receptor 4

Up/down

[76, 81, 82]

Yes

FGFR2

Fibroblast growth factor receptor 2

Up

[72, 76]

Yes

FGFR4

Fibroblast growth factor receptor 4

Up

[22, 73, 76, 88, 89]

Yes

FLNB

Filamin B, beta

Down

[76, 82]

Yes

FNBP1

Formin-binding protein 1

Down

[22, 75, 76]

?

FOXF1

Forkhead box protein F1

Up

[22, 72, 74, 76, 81]

Yes

FOXO1

Forkhead box O1

Up

[75, 76]

Yes

GADD45A

Growth arrest and DNA-damage-inducible protein GADD45 alpha

Up

[73, 76, 81]

Yes

GRAF

GTPase regulator associated with FAK

Up

[22, 72]

Yes

GTF3C1

General transcription factor 3C

Up

[72, 81]

Yes

H19

Imprinted maternally expressed gene, untranslated mRNA

Up

[5, 79]

Yes

HDAC5

Histone deacetylase 5

Up

[73, 76]

Yes

HUMMLC2B

Myosin regulatory light chain 2, skeletal muscle isoform

Down

[72, 73]

Yes

IGF2

Insulin-like growth factor II

Up

[5, 75]

Yes

IGFBP3

IGF-binding protein 3

Down

[73, 81]

Yes

IGFBP5

IGF-binding protein 5

Up

[5]

Yes

IL4R

Interleukin 4 receptor

Up

[72, 73, 75, 76]

Yes

JAKMIP2

Janus kinase and microtubule-interacting protein 2

Up

[7274, 76]

Yes

KCNN3

Small conductance calcium-activated potassium channel protein 3

Up

[73, 74, 81]

Yes

KCNS3

Potassium voltage-gated channel subfamily S member 3

Up

[73, 74]

?

LRRFIP2

Leucine-rich repeat (in FLII) interacting protein 2

Up

[72, 74]

Yes

MARCH3

Membrane-associated RING finger protein 3

Up

[73, 81]

Yes

MCAM

Melanoma cell adhesion molecule

Up

[73, 81]

Yes

MEG3

Maternally expressed 3

Up

[7375]

?

MN1

Meningioma (disrupted in balanced translocation) 1

Up

[73, 76]

Yes

MET

Hepatocyte growth factor receptor

Up

[73, 76, 81, 9092]

Yes

MTUS2

Microtubule associated tumor suppressor candidate 2

Up

[72, 76]

Yes

MYBPH

Myosin-binding protein H

Up/down

[5, 72, 75]

Yes

MYCN

N-MYC proto-oncogene protein

Up

[72, 73, 76, 78, 81]

Yes

MYH8

Myosin, heavy chain 8, skeletal muscle, perinatal

Up/down

[5, 72]

Yes

MYL1

Myosin, light chain 1, alkali; skeletal, fast

Up/down

[5, 79]

Yes

MYL4

Myosin, light chain 4, alkali; atrial, embryonic

Up/down

[5, 72]

Yes

MYOD

Myoblast determination protein 1

Up

[5, 73, 76, 81]

Yes

MYOG

Myogenin (myogenic factor 4)

Up

[5, 90]

Yes

NEBL

Nebulette

Up/down

[72, 73, 76, 81]

Yes

NELL1

NEL-like protein 1

Up

[22, 7274, 76]

Yes

NHLH1

Nescient helix loop helix 1

Up

[22, 76]

Yes

NPTX2

Neuronal pentraxin II

Down

[76, 81]

Yes

NRCAM

Neuronal cell adhesion molecule

Up

[7274]

Yes

OLIG2

Oligodendrocyte transcription factor 2

Up

[22, 74]

?

PALMD

Palmdelphin

Down

[72, 76]

Yes

PBK

PDZ-binding kinase

Up

[73, 76]

Yes

PCDH7

Protocadherin 7

Up

[76, 82]

Yes

PDZRN3

PDZ domain containing ring finger 3

Up

[74, 76]

Yes

PGBD5

PiggyBac transposable element-derived protein 5

Up

[22, 72, 74]

Yes

PHF17

PHD finger protein 17

Up

[74, 76]

Yes

PIPOX

Pipecolic acid oxidase

Up

[22, 72, 74, 76]

Yes

PKP1

Plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)

Up

[72, 76]

Yes

PLAG1

Pleiomorphic adenoma gene 1 protein

Down

[75, 81]

Yes

PLK2

Polo-like kinase 2

Down

[73, 76]

Yes

PODXL

Podocalyxin-like protein 1

Up

[22, 74, 76]

Yes

POU4F1

Brain-specific homeobox/POU domain protein 3A

Up

[72, 73, 76]

Yes

PPARGC1A

Peroxisome proliferator-activated receptor gamma, coactivator 1 alpha

Up

[22, 76]

Yes

PRKAR2B

Protein kinase, cAMP-dependent, regulatory, type II, beta

Up

[73, 81, 82]

Yes

PRKCA

Protein kinase C, alpha

Up

[73, 76]

Yes

PSEN2

Presenilin 2 (Alzheimer’s disease 4)

Up

[73, 74]

?

PTHLT

Parathyroid hormone-like hormone

Up

[76, 82]

Yes

QDPR

Quinoid dihydropteridine reductase

Up

[74, 81]

Yes

RASSF4

Ras association (RalGDS/AF-6) domain family 4

Up

[72, 74, 76]

Yes

RRP22

Ras-like protein family member 10A, on chm 22

Up

[73, 74]

?

RYR1

Skeletal muscle-type ryanodine receptor

Up

[5, 74]

Yes

RYR3

Brain-type ryanodine receptor

Up

[74, 76, 81]

Yes

SLC24A3

Solute carrier family 24 (sodium/potassium/calcium exchanger), member 3

Up

[74, 76]

Yes

SIX1

SIX homeobox 1

Up

[5, 75]

Yes

SOX14

SRY (sex determining region Y)-box 14

Up

[22, 76]

Yes

STX11

Syntaxin 11

Up

[76, 82]

Yes

SULF1

Sulfatase 1

Up

[73, 76]

Yes

SVIL

Supervillin

Down

[72, 76]

Yes

TCF712

Transcription factor 7-like 2 (T-cell specific, HMG-box)

Up

[73, 81]

Yes

TGFB1

Transforming growth factor, beta 1

Up

[5, 76]

Yes

TFAP2B

Transcription factor AP-2 beta

Up

[22, 72]

Yes

TIAF1

TGF-beta-1-induced antiapoptotic factor 1

Up

[73, 74]

?

TM4SF10

Transmembrane 4 superfamily member 10

Up

[73, 81]

Yes

TNFAIP3

Tumor necrosis factor, alpha-induced protein 3

Up

[73, 76]

Yes

TNNC2

Troponin C type 2 (fast)

Up/down

[5, 72, 73, 79]

Yes

TNNI2

Troponin I type 2 (skeletal, fast)

Up/down

[5, 72]

Yes

TNNT2

Troponin T type 2 (cardiac)

Up

[5, 79]

Yes

TNNT3

Troponin T type 3 (skeletal, fast)

Down

[72, 79]

Yes

TRAM2

Translocation-associated membrane protein 2

Up

[73, 76]

Yes

TSC22D2

TSC22 domain family, member 2

Up

[74, 76]

Yes

UBE2G2

Ubiquitin-conjugating enzyme E2G 2 (UBC7 homolog, yeast)

Up

[22, 76]

Yes

WSCD1

WSC domain-containing protein 1

Up

[22, 74]

?

WVA5A

Von Willebrand factor A domain containing 5A

Up

[7274]

Yes

  1. Summary of genes found to be differentially regulated in more than one reference in ARMS tumors and/or cell lines, or by PAX3-FOXO1 overexpression, in various cell types. Gene name and description are indicated and also the relative expression in ARMS or PAX3-FOXO1. Also indicated is whether the study indicates that these genes are downstream of PAX3-FOXO1 expression. Genes indicated in bold will be further discussed.